Contacts of the strand formed by residues 260 - 268 (chain A) in PDB entry 5V6Y
Residue contacts within the protein are
derived with the CSU software (Sobolev V., Sorokine A.,
Prilusky J., Abola E.E. and Edelman M. (1999) Automated
analysis of interatomic contacts in proteins.
Bioinformatics, 15, 327-332). A
short description of the analytical approach
is given at the end of the page.
Note:
Non-standard 3 letter residue
codes indicate a heterogroup. To identify
and analyse, use LPC software
Legend:
Dist - nearest distance (Å) between atoms of two residues
Surf - contact surface area (Å2) between two residues
HB - hydrophilic-hydrophilic contact (hydrogen bond)
Arom - aromatic-aromatic contact
Phob - hydrophobic-hydrophobic contact
DC - hydrophobic-hydrophilic contact (destabilizing contact)
+/- - indicates presence/absence of a specific contacts
* - indicates residues forming contacts by their side chain
(including CA atoms)
Residues in contact with PHE 260 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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113A GLU 4.5 0.5 - - - +
114A ALA* 5.0 1.6 - - - -
115A LEU* 5.4 0.4 + - - +
157A TYR* 3.5 31.4 + - + +
160A TRP* 3.3 43.1 - + + +
161A PRO* 4.9 1.6 - - - +
169A TYR* 5.8 0.2 - - - -
170A ALA* 3.7 23.6 - - + -
258A LYS 3.6 2.2 + - - -
259A PRO* 1.3 73.7 - - - +
261A VAL* 1.3 62.6 + - - +
330A GLU* 3.2 30.1 - - + -
331A ILE 4.2 2.9 - - - -
332A MET* 3.5 30.7 - - + -
333A PRO* 4.2 11.0 - - + -
338A MET* 4.5 2.9 - - + -
341A PHE* 3.8 20.6 - + - -
342A TRP* 3.6 25.4 - + + -
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Residues in contact with VAL 261 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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66A HIS* 3.5 5.4 - - - -
94A PHE* 5.2 6.3 - - + -
112A VAL* 3.6 24.7 - - + -
113A GLU 3.4 13.5 - - - +
114A ALA* 4.5 3.6 - - + -
259A PRO 3.7 12.1 - - - +
260A PHE* 1.3 71.0 - - - +
262A GLY* 1.3 62.2 + - - +
263A VAL* 5.4 0.7 - - + -
326A ALA* 3.3 41.7 - - + +
330A GLU 2.8 21.2 + - - +
331A ILE* 3.5 14.8 - - + +
332A MET* 2.9 27.1 + - - +
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Residues in contact with GLY 262 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
65A ALA* 4.5 5.6 - - - -
66A HIS* 3.7 1.6 - - - -
112A VAL* 3.6 3.3 - - - +
113A GLU* 2.6 47.9 + - - +
157A TYR* 4.7 3.8 + - - -
260A PHE 3.7 3.0 + - - -
261A VAL* 1.3 74.9 - - - +
263A VAL* 1.3 62.2 + - - +
264A LEU 4.0 0.4 - - - -
332A MET* 3.6 20.9 - - - -
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Residues in contact with VAL 263 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
65A ALA* 4.0 2.0 - - - +
66A HIS* 2.9 51.8 + - + +
94A PHE* 4.9 4.7 - - + -
95A THR* 4.8 9.0 - - + +
98A ALA* 3.9 20.2 - - + -
99A VAL* 5.1 0.2 - - + -
109A PRO* 3.8 28.5 - - + -
111A ALA 3.3 15.3 - - - +
112A VAL* 4.3 18.8 - - + -
261A VAL* 5.4 0.7 - - + -
262A GLY* 1.3 75.4 - - - +
264A LEU* 1.3 62.3 + - - +
265A SER* 2.9 15.4 + - - +
331A ILE* 4.5 8.1 - - + -
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Residues in contact with LEU 264 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13A ILE* 4.9 7.6 - - + -
17A LYS* 4.3 21.1 - - + -
63A PHE* 4.3 20.4 - - + -
64A TRP* 3.7 30.3 - - - +
65A ALA* 4.3 2.6 - - - +
109A PRO* 3.7 0.2 - - - +
110A ILE* 2.6 46.6 + - + +
111A ALA* 2.9 17.9 + - + +
113A GLU* 3.5 26.6 + - + +
262A GLY 4.0 2.0 + - - -
263A VAL* 1.3 70.0 - - - +
265A SER* 1.3 54.3 + - - +
301A LEU* 3.7 30.3 - - + -
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Residues in contact with SER 265 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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63A PHE* 3.2 10.8 - - - -
64A TRP 2.7 36.8 + - - +
66A HIS* 3.8 4.2 - - - +
69A PHE* 3.4 18.8 - - - -
99A VAL* 3.3 28.8 - - - +
107A ALA* 4.0 4.0 - - - -
108A TYR 3.2 11.0 - - - -
109A PRO* 4.1 0.3 - - - +
110A ILE* 4.5 0.7 - - - -
263A VAL* 2.9 17.5 + - - +
264A LEU* 1.3 73.2 + - - +
266A ALA* 1.3 60.0 + - - +
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Residues in contact with ALA 266 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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61A ILE* 4.0 4.3 - - + -
62A ILE 3.3 5.2 - - - -
63A PHE* 3.5 32.3 - - + -
81A ILE* 5.5 0.2 - - - +
107A ALA* 3.3 3.9 - - - -
108A TYR* 2.7 47.6 + - + +
110A ILE* 4.5 2.5 - - + -
265A SER* 1.3 74.2 - - - +
267A GLY* 1.3 59.4 + - - +
268A ILE* 4.4 0.3 + - - +
282A LEU* 4.0 21.4 - - + +
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Residues in contact with GLY 267 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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61A ILE* 3.2 8.2 - - - +
62A ILE* 2.9 40.1 + - - +
69A PHE* 3.4 19.7 - - - -
78A LEU* 4.4 3.4 - - - -
106A ILE 4.1 6.1 - - - -
107A ALA* 3.9 7.0 - - - -
266A ALA* 1.3 74.8 - - - +
268A ILE* 1.3 63.0 + - - -
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Residues in contact with ILE 268 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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60A ASP 3.4 10.5 - - - +
61A ILE* 4.9 0.4 - - + -
78A LEU* 3.4 9.1 - - - +
79A ALA* 2.7 43.1 + - + +
80A GLU 6.0 1.1 - - - +
81A ILE* 4.4 20.6 - - + +
106A ILE 4.7 3.0 + - - -
108A TYR* 4.5 10.1 - - + -
266A ALA 5.2 0.4 - - - +
267A GLY* 1.3 76.5 - - - +
269A ASN* 1.3 67.8 + - - +
272A SER* 4.9 2.7 - - - -
275A LYS* 4.1 35.7 - - + +
278A ALA* 3.8 27.1 - - + -
279A LYS* 4.3 8.7 - - + +
282A LEU* 4.5 9.9 - - + -
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A short description of the
analytical approach
The contact analysis used in this page
is based upon the approach
developed in:
Sobolev V., Wade R.C., Vriend G.
and Edelman M. PROTEINS (1996)
25, 120-129.
Contact legitimacy depends on the hydrophobic-hydrophilic
properties of the contacting atoms. In order to
define it, for each inter-atomic contact,
eight atom classes have been introduced:
I Hydrophilic - N and O that can donate and accept hydrogen bonds
(e.g., oxygen of hydroxyl group of Ser. or Thr)
II Acceptor - N or O that can only accept a hydrogen bond
III Donor - N that can only donate a hydrogen bond
IV Hydrophobic - Cl, Br, I and all C atoms that are not in
aromatic rings and do not have a covalent bond to
a N or O atom
V Aromatic - C in aromatic rings irrespective of any other
bonds formed by the atom
VI Neutral - C atoms that have a covalent bond to at least one
atom of class I or two or more atoms from class II
or III; atoms; S, F, P, and metal atoms in all cases
VII Neutral-donor - C atoms that have a covalent bond with only one
atom of class III
VIII Neutral-acceptor - C atoms that have a covalent bond with only
one atom of class II
For each pair of contacts the state of legitimacy
is shown below:
Legend:
+, legitimate
-, illegitimate
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Atomic class I II III IV V VI VII VIII
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I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
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Warning!
Atom classes for heterogroups are automatically
assigned based on the atomic coordinates. However, in
three cases (see below) the automatic assignment
is currently ambiguous. In these
cases, the user is advised to manually analyse
the full list of contacts using
LPC software.
1. Carbon atoms belonging to a 4-, 5- or 6-member ring are
considered "aromatic" (Class V) if the ring is approximately
planar, and "hydrophobic" (Class IV) or "neutral" (Classes
VI, VII, VIII) if the ring is non-planar.
2. The oxygen atom of a carbonyl or hydroxy group is considered
"hydroxy" (Class I) if the CO bond is longer than 1.29 Å, and
"carbonyl" (Class II) if shorter.
3. All nitrogen atoms are considered "hydrophilic" (Class I).
Please E-mail any
questions and/or suggestions concerning this page to
Vladimir.Sobolev@weizmann.ac.il